data_2PE5 # _model_server_result.job_id aeRGq8eHdueh6eLWjh-_Xw _model_server_result.datetime_utc '2024-11-05 23:17:49' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2pe5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":903}' # _entry.id 2PE5 # _exptl.entry_id 2PE5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 301.249 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-nitrophenyl beta-D-galactopyranoside' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 2PE5 _cell.length_a 253.08 _cell.length_b 253.08 _cell.length_c 203.247 _cell.Z_PDB 54 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PE5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,D,E,G,H 1 1 C,F,I 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 146.115806 135.498 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 H N N ? 3 I N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order hydrog 'DG-DC PAIR' hydrog1 A N1 DG 5 D DG 6 1_555 B O2 DC 16 E DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog2 A O4 DT 6 D DT 7 1_555 B N6 DA 15 E DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog3 A N1 DG 7 D DG 8 1_555 B N3 DC 14 E DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog4 A N1 DA 8 D DA 9 1_555 B N3 DT 13 E DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N1 DG 9 D DG 10 1_555 B N3 DC 12 E DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N2 DG 9 D DG 10 1_555 B O2 DC 12 E DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O6 DG 9 D DG 10 1_555 B N4 DC 12 E DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog8 A N2 DG 9 D DG 10 1_555 B O2 DT 13 E DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DC 10 D DC 11 1_555 B N1 DG 11 E DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 DC 10 D DC 11 1_555 B O6 DG 11 E DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 DC 10 D DC 11 1_555 B N2 DG 11 E DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N1 DG 11 D DG 12 1_555 B N3 DC 10 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N2 DG 11 D DG 12 1_555 B O2 DC 10 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O6 DG 11 D DG 12 1_555 B N4 DC 10 E DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N3 DC 12 D DC 13 1_555 B N1 DG 9 E DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N4 DC 12 D DC 13 1_555 B O6 DG 9 E DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O2 DC 12 D DC 13 1_555 B N2 DG 9 E DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N3 DT 13 D DT 14 1_555 B N1 DA 8 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A O4 DT 13 D DT 14 1_555 B N6 DA 8 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog20 A O2 DC 14 D DC 15 1_555 B N2 DG 7 E DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog21 A N1 DA 15 D DA 16 1_555 B N1 DG 5 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_8_PAIR hydrog22 A N6 DA 15 D DA 16 1_555 B O6 DG 5 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DA 15 D DA 16 1_555 B N3 DT 6 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N6 DA 15 D DA 16 1_555 B O4 DT 6 E DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog25 A O2 DC 16 D DC 17 1_555 B N1 DG 5 E DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog26 A N1 DA 18 D DA 19 1_555 B N3 DT 3 E DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A N3 DT 19 D DT 20 1_555 B N1 DA 2 E DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A O4 DT 19 D DT 20 1_555 B N6 DA 2 E DA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog29 A N3 DT 20 D DT 21 1_555 B N1 DA 1 E DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog30 C N1 DA 2 F DA 3 1_555 C N6 DA 17 F DA 18 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog31 C N6 DA 2 F DA 3 1_555 C N7 DA 17 F DA 18 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog32 C N2 DG 7 F DG 8 1_555 C N3 DC 14 F DC 15 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N1 DA 8 F DA 9 1_555 C N3 DT 13 F DT 14 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N6 DA 8 F DA 9 1_555 C O4 DT 13 F DT 14 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C N1 DG 9 F DG 10 1_555 C N3 DC 12 F DC 13 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N2 DG 9 F DG 10 1_555 C O2 DC 12 F DC 13 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C O6 DG 9 F DG 10 1_555 C N4 DC 12 F DC 13 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog38 C N2 DG 9 F DG 10 1_555 C O2 DT 13 F DT 14 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 C N3 DC 10 F DC 11 1_555 C N1 DG 11 F DG 12 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 C N4 DC 10 F DC 11 1_555 C O6 DG 11 F DG 12 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 C O2 DC 10 F DC 11 1_555 C N2 DG 11 F DG 12 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 C N1 DG 11 F DG 12 1_555 C N3 DC 10 F DC 11 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 C N2 DG 11 F DG 12 1_555 C O2 DC 10 F DC 11 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 C O6 DG 11 F DG 12 1_555 C N4 DC 10 F DC 11 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 C N3 DC 12 F DC 13 1_555 C N1 DG 9 F DG 10 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog46 C N4 DC 12 F DC 13 1_555 C O6 DG 9 F DG 10 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog47 C O2 DC 12 F DC 13 1_555 C N2 DG 9 F DG 10 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog48 C N3 DT 13 F DT 14 1_555 C N1 DA 8 F DA 9 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog49 C O4 DT 13 F DT 14 1_555 C N6 DA 8 F DA 9 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DG MISPAIR' hydrog50 C O2 DT 13 F DT 14 1_555 C N2 DG 9 F DG 10 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog51 C N3 DC 14 F DC 15 1_555 C N2 DG 7 F DG 8 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog52 C N6 DA 17 F DA 18 1_555 C N1 DA 2 F DA 3 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_5_PAIR hydrog53 C N7 DA 17 F DA 18 1_555 C N6 DA 2 F DA 3 17_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C12 H15 N O8' _chem_comp.formula_weight 301.249 _chem_comp.id 145 _chem_comp.mon_nstd_flag n _chem_comp.name '2-nitrophenyl beta-D-galactopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms '1-O-[O-NITROPHENYL]-BETA-D-GALACTOPYRANOSE;2-nitrophenyl beta-D-galactoside;2-nitrophenyl D-galactoside;2-nitrophenyl galactoside' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C1 C2 145 sing 1 n n C1 O5 145 sing 2 n n C1 O1 145 sing 3 n n C1 H1 145 sing 4 n n C2 O2 145 sing 5 n n C2 C3 145 sing 6 n n C2 H2 145 sing 7 n n O2 HO2 145 sing 8 n n C3 O3 145 sing 9 n n C3 C4 145 sing 10 n n C3 H3 145 sing 11 n n O3 HO3 145 sing 12 n n C4 O4 145 sing 13 n n C4 C5 145 sing 14 n n C4 H4 145 sing 15 n n O4 HO4 145 sing 16 n n C5 C6 145 sing 17 n n C5 O5 145 sing 18 n n C5 H5 145 sing 19 n n C6 O6 145 sing 20 n n C6 H61 145 sing 21 n n C6 H62 145 sing 22 n n O6 HO6 145 sing 23 n n O1 C1' 145 sing 24 n n C1' C2' 145 doub 25 n y C1' C6' 145 sing 26 n y C2' C3' 145 sing 27 n y C2' N1' 145 sing 28 n n C3' C4' 145 doub 29 n y C3' H3' 145 sing 30 n n C4' C5' 145 sing 31 n y C4' H4' 145 sing 32 n n C5' C6' 145 doub 33 n y C5' H5' 145 sing 34 n n C6' H6' 145 sing 35 n n N1' O2' 145 sing 36 n n N1' O3' 145 doub 37 n n # _pdbx_chem_comp_identifier.comp_id 145 _pdbx_chem_comp_identifier.identifier 1-O-[O-nitrophenyl]-b-D-galactopyranose _pdbx_chem_comp_identifier.type 'IUPAC CARBOHYDRATE SYMBOL' _pdbx_chem_comp_identifier.program PDB-CARE _pdbx_chem_comp_identifier.program_version 1 # _atom_sites.entry_id 2PE5 _atom_sites.fract_transf_matrix[1][1] 0.003951 _atom_sites.fract_transf_matrix[1][2] 0.002281 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004563 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00492 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code G 3 145 A 1 901 901 145 DRG . H 3 145 B 1 902 902 145 DRG . I 3 145 C 1 903 903 145 DRG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 145 . . . I 3 42.887 81.383 60.135 1 14.49 ? C1 145 903 C 1 HETATM 2 C C2 145 . . . I 3 41.686 80.459 60.299 1 12.81 ? C2 145 903 C 1 HETATM 3 O O2 145 . . . I 3 40.956 80.433 59.098 1 10.6 ? O2 145 903 C 1 HETATM 4 C C3 145 . . . I 3 40.755 80.953 61.399 1 14 ? C3 145 903 C 1 HETATM 5 O O3 145 . . . I 3 39.694 80.005 61.587 1 15.02 ? O3 145 903 C 1 HETATM 6 C C4 145 . . . I 3 41.492 81.215 62.732 1 14.74 ? C4 145 903 C 1 HETATM 7 O O4 145 . . . I 3 41.727 79.988 63.459 1 16.75 ? O4 145 903 C 1 HETATM 8 C C5 145 . . . I 3 42.811 81.97 62.488 1 14.33 ? C5 145 903 C 1 HETATM 9 C C6 145 . . . I 3 43.739 81.89 63.687 1 13.9 ? C6 145 903 C 1 HETATM 10 O O6 145 . . . I 3 44.925 82.589 63.341 1 14.9 ? O6 145 903 C 1 HETATM 11 O O5 145 . . . I 3 43.588 81.461 61.382 1 14.23 ? O5 145 903 C 1 HETATM 12 O O1 145 . . . I 3 43.871 80.749 59.316 1 17.42 ? O1 145 903 C 1 HETATM 13 C C1' 145 . . . I 3 44.074 81.216 58.062 1 20.11 ? C1' 145 903 C 1 HETATM 14 C C2' 145 . . . I 3 45.451 81.43 57.913 1 21.63 ? C2' 145 903 C 1 HETATM 15 C C3' 145 . . . I 3 46.26 80.599 57.146 1 22.23 ? C3' 145 903 C 1 HETATM 16 C C4' 145 . . . I 3 45.707 79.519 56.491 1 23.22 ? C4' 145 903 C 1 HETATM 17 C C5' 145 . . . I 3 44.344 79.293 56.608 1 22.97 ? C5' 145 903 C 1 HETATM 18 C C6' 145 . . . I 3 43.551 80.136 57.367 1 21.82 ? C6' 145 903 C 1 HETATM 19 N N1' 145 . . . I 3 46.067 82.44 58.516 1 22.73 ? N1' 145 903 C 1 HETATM 20 O O2' 145 . . . I 3 47.48 82.601 58.323 1 23.17 ? O2' 145 903 C 1 HETATM 21 O O3' 145 . . . I 3 45.357 83.36 59.329 1 23.06 ? O3' 145 903 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #